Technical Quarto data report on cumulative known occupancy and corridor-scale discovery of perennial pepperweed (Lepidium latifolium) along the Lower Owens River Project (LORP), Owens Valley, California.
Live site: inyo-gov.github.io/noxious-weeds
Workplan: FY 2026–2027 LORP Work Plan and Budget (PDF)
- Abstract / introduction / methods — academic framing of estimands (cumulative known occupancy; herbicide out of scope)
- Interactive Leaflet map — detections by year (
2018–current_year), river channels, 2026 east/west gap lines - Abundance, reach, and river-mile analyses — LORP Reaches 1–6 and mile summaries
- Occupancy & cumulative discovery — forecasts toward corridor saturation (linear / asymptotic / logistic / recent-trajectory) plus fast vs low step-pulse scenarios
- 0.1-mi cumulative heatmap — corridor discovery geography (white = never detected; persists after first detection)
- 2026 RAS applications — unoccupied river miles (250 m corridor filter), bank notes, Field Maps gap-line exports
- References — cited ecology and LORP sources
- Downloads — GeoJSON / KML of mapped sites
Output formats: HTML (docs/) for GitHub Pages and Word (docs/index.docx).
| Layer | Source |
|---|---|
| Pepperweed sites | Noxious Weeds 2025 View |
| High-water floodplain | north / south |
| River channels | owens_river_feature |
| River miles | data/LORP_RiverMiles_revised.shp |
| Reaches | AGOL LORP reach polygons (Reaches 1–6) |
Pepperweed and reference layers are pulled live at render time. River miles ship with the repo.
noxious-weeds/
├── index.qmd # Main report
├── _quarto.yml # Website config → docs/
├── styles.css
├── export_survey_nav.R # Field Maps / floodplain negative-space export
├── render_pepperweed_report.R
├── update_year.R # Bump params$current_year
├── setup_r_packages.R
├── data/ # River-mile shapefile
├── exports/survey_nav_2026/ # GeoJSON + shapefile zip for Field Maps
└── docs/ # Rendered site (GitHub Pages)
Optional scripts (not required for the HTML report): lepidium_app.py, arcfetch_storeduckdb.py.
Prerequisites: R ≥ 4.0, Quarto CLI, network access to ArcGIS Online.
source("setup_r_packages.R")Or install from r_requirements.txt / the packages listed in setup_r_packages.R.
Python deps in requirements.txt are only needed for optional utilities (not Quarto HTML).
quarto render index.qmdOr both HTML and Word:
source("render_pepperweed_report.R")Refresh Field Maps navigation layers (also runs from the report if the script is present):
Rscript export_survey_nav.RRscript update_year.R 2026
quarto render index.qmdParameters in index.qmd:
current_year— latest survey year (default2025)start_year— start of time series (default2018)
Caveat (through end of July 2026): treat gap lines as a draft for Field Maps; confirm against the river-mile recommendation tables before field use.
export_survey_nav.R builds east/west parallel gap lines:
- River-mile centerline (RM 0–60)
- Detections within 250 m assigned to East / West bank
- Empty 0.1-mi segment×bank runs dissolved; keep stretches ≥400 m
- Offset polylines 50 m from centerline
| Bank | Color | Pattern |
|---|---|---|
| East | Sky blue #0077BB |
Solid |
| West | Orange #EE7733 |
Dashed |
(Pattern differs so meaning is not color-only.) Outputs: exports/survey_nav_2026/ → copied to docs/exports/ on render.
GitHub Pages is configured for the docs/ folder → inyo-gov.github.io/noxious-weeds.
Local preview:
cd docs && python -m http.server 8000- Sites more than 250 m from a river-mile marker are excluded from corridor occupancy so off-channel ditch/field points do not falsely occupy a mile.
- Abundance class 200 means ≥200 (dense patches are not stem-counted).
- Occupancy forecasts are descriptive discovery models, not biological invasion rates; more RAS effort in empty miles raises known occupancy even without new colonization.
- See
WORKLOG.mdfor recent planning context and open follow-ups.
Inyo County Water Department — LORP / noxious weeds monitoring.
See LICENSE.